Image Drift Research Articles

Lateral drift correction in time-laps images by the particle-tracking algorithm

In long-term time-laps imaging of living cells, a significant lateral drift of the fluorescently labeled structures is often observed due to many reasons including superfusion of solution, temperature gradients, bolus addition of pharmacological agents and cell motility. We have detected lateral drift in long-term time-laps confocal imaging by tracking fluorescent puncta, which represent single exocytotic vesicles expressing synaptopHluorin (spH), a pH sensitive green fluorescence protein. Following the initial increase in fluorescence intensity due to alkalinization of vesicle lumen, the spH fluorescent puncta dimmed, which may be attributed to the resealing of the fusion pore and subsequent slow reacidification of the vesicle, or alternatively the dimming may be due to a significant lateral drift of the vesicle out of the region of interest (ROI). We identified and compensated the lateral drift by tracking particles present in the confocal images, without any additional mechanical and/or optical hardware components. The peak of the Gaussian two-dimensional (2D) curve fitted to the fluorescent particle intensity profile was recorded as the X and Y coordinates of the vesicle in each frame. The resulting coordinates of vesicle positions were averaged and rounded to the nearest pixel value, which was used to correct the drift in the time-laps images. In drift corrected time-laps images, the vesicle remained enclosed by the ROI, and the time dependent changes of spH fluorescence intensity averaged from the ROI remained at a constant level, revealing that endocytosis with subsequent slow reacidification of vesicles was an unlikely event.

Drift and spatial distortion elimination in atomic force microscopy images by the digital image correlation technique

The characterization of nanomaterials and nanostructures on the nanoscale has been a tremendous challenge for many existing testing and measurement techniques. With the rapid development of microfabrication and nanofabrication technologies, appropriate and accurate tools for nanometrology and nanomechanical testing must be developed. In this study, a recently developed methodology for scanning electron microscopy (SEM) image correction has been successfully adapted to correct the drift and spatial distortion of atomic force microscopy (AFM) images. Using this approach with a standard AFM sample stage, the errors in AFM images, artificial strains for zero deformation, have been reduced to 150×10−6 ± 1300×10−6. When using a sample stage with closed-loop control, the method reduces errors to 200×10−6 ± 1000×10−6, confirming that the SEM-based approach is capable of removing much of the distortion present in typical AFM images.

Restoring the Suzaku Source Position Accuracy and Point-Spread function

Abstract We present an empirical correction of sky coordinates of X-ray photons obtained with the X-ray Imaging Spectrometer (XIS) aboard the Suzaku satellite to improve the source position accuracy and restore the point-spread function (PSF). The XIS images are known to have an uncertainty in position of up to $1′$, and to show considerable degradations of the PSF. These problems are caused by a drifting of the satellite attitude due to thermal distortion of the side panel #7, where the attitude control system is mounted. We found that the position error averaged over a pointing observation can be largely reduced by using the relation between the deviation of the source position in the DETX direction and the ecliptic latitude of the pointing target. We parameterized the wobbling of the source position synchronized with the 96-minute satellite orbital period with temperatures of onboard radiators and elapsed time since the night-day transition of the spacecraft. We developed software, aeattcor, to correct the image drift using these parameters, and applied it to 27 point-source images taken in the Suzaku initial science-operation phase. We show that the radius of the 90% error circle of the source position was reduced to $19′$ and the PSF was sharpened. These improvements have enhanced the scientific capability of the Suzaku XIS.

The Stability of the Point‐Spread Function of the Advanced Camera for Surveys on the Hubble Space Telescope and Implications for Weak Gravitational Lensing

(abridged) We examine the spatial and temporal stability of the HST ACS Wide Field Camera (WFC) point spread function (PSF) using the two square degree COSMOS survey. We show that stochastic aliasing of the PSF necessarily occurs during `drizzling'. This aliasing is maximal if the output pixel scale is equal to the input pixel scale of 0.05''. We show that this source of PSF variation can be significantly reduced by choosing a Gaussian drizzle kernel and by setting the output pixel size to 0.03''. We show that the PSF is temporally unstable, most likely due to thermal fluctuations in the telescope's focus. We find that the primary manifestation of this thermal drift in COSMOS images is an overall slow periodic focus change. Using a modified version of TinyTim, we create undistorted stars in a 30x30 grid across the ACS WFC CCDs. These PSF models are created for telescope focus values in the range -10 microns to +5 microns, thus spanning the allowed range of telescope focus values. We then use the approximately ten well measured stars in each COSMOS field to pick the best-fit focus value for each field. The TinyTim model stars are then used to perform PSF corrections for weak lensing allowing systematics due to incorrectly modeled PSFs to be greatly reduced. We have made the software for PSF modeling using our modified version of TinyTim available to the astronomical community. We show the effects of Charge Transfer Efficiency (CTE) degradation, which distorts the object in the readout direction, mimicking a weak lensing signal. We derive a parametric correction for the effect of CTE on the shapes of objects in the COSMOS field as a function of observation date, position within the ACS WFC field, and object flux.

Rigid and non-rigid face motion tracking by aligning texture maps and stereo 3D models

Accurate rigid and non-rigid tracking of faces is a challenging task in computer vision. Recently, appearance-based 3D face tracking methods have been proposed. These methods can successfully tackle the image variability and drift problems. However, they may fail to provide accurate out-of-plane face motions since they are not very sensitive to out-of-plane motion variations. In this paper, we present a framework for fast and accurate 3D face and facial action tracking. Our proposed framework retains the strengths of both appearance and 3D data-based trackers. We combine an adaptive appearance model with an online stereo-based 3D model. We provide experiments and performance evaluation which show the feasibility and usefulness of the proposed approach.

Improvement of Fresnel zone plate beam-profile monitor and application to ultralow emittance beam profile measurements

We describe the improvements of a Fresnel zone plate (FZP) beam-profile monitor, which is being developed at the KEK-ATF damping ring to measure ultralow emittance electron-beam profiles. This monitor, which is designed to have a submicrometer spatial resolution, is based on x-ray imaging optics composed of two FZPs. Various improvements were performed to the old setup. First, a new crystal monochromator was introduced to suppress the beam image drift. Second, the two FZP folders were improved in order to realize a precise beam-based alignment during x-ray imaging. Third, a fast mechanical shutter was installed to achieve a shorter time resolution, and an x-ray mask system was also installed to obstruct direct synchrotron radiation through the FZPs. These improvements could make beam-profile measurements more precise and reliable. The beam profiles with less than 50 m horizontal beam size and less than 6 m vertical beam size could be measured within a 1 ms time duration. Furthermore, measurements of the damping time and the coupling dependence of the ATF damping ring were successfully carried out with this upgraded FZP monitor.

Focused ion beam (FIB) milling of electrically insulating specimens using simultaneous primary electron and ion beam irradiation

There is currently great interest in combining focused ion beam (FIB) and scanning electron microscopy technologies for advanced studies of polymeric materials and biological microstructures, as well as for sophisticated nanoscale fabrication and prototyping. Irradiation of electrically insulating materials with a positive ion beam in high vacuum can lead to the accumulation of charge, causing deflection of the ion beam. The resultant image drift has significant consequences upon the accuracy and quality of FIB milling, imaging and chemical vapour deposition. A method is described for suppressing ion beam drift using a defocused, low-energy primary electron beam, leading to the derivation of a mathematical expression to correlate the ion and electron beam energies and currents with other parameters required for electrically stabilizing these challenging materials.

Probing adsorption sites on thin oxide films by dynamic force microscopy

Site specific atomically resolved dynamic force spectroscopy measurements were performed on a thin MgO film grown on Ag(001). The microscope is operated in ultrahigh vacuum at low temperature to ensure defined imaging condition, high stability, and drift reduction. Atomically resolved dynamic force microscopy images have been combined with site specific frequency shift versus distance measurements. The frequency shift is measured as a function of z and the lateral displacement. With these measurement characteristics the authors are currently probing inequivalent surface sites on thin MgO films to extract atomic-scale information on surface chemical reactivity and possible adsorption sites for metal atoms and small clusters.

Water — A Clean “Glue” to Attach Hydrophilic Plates to an AFM Sample Stage

Abstract Attaching a sample to the instrument's sample stage is commonly the first step in the operation of an AFM. For our commercial Digital Instruments Multimode AFM, a sample is usually attached to a magnetic sample puck by double-sided tape, the sample puck is then placed on the instrument’s magnetic sample stage, and analysis can begin. The use of double-sided tape, however, has unpleasant consequences. First, the surface of the sample puck becomes quite sticky due to residual glue from the double-sided tape ! removing the sticky glue is not a happy job. One cannot just throw a soiled sample puck away! Second, double-sided tape does not always give satisfactory mechanical stability during AFM operation, especially when high resolution imaging is being carried out. Sometimes the tape-mounted sample will creep slowly, which can cause significant drift of AFM images. This is because the tapes and their adhesive films are made of pressure sensitive materials that tend to change shape when pressure and/or temperature vary.

A STEM/EELS method for mapping iron valence ratios in oxide minerals

The valence state of iron in minerals has useful applications in the geosciences for estimating redox conditions during mineral formation or re-equilibration. STEM/EELS techniques offer the advantage over other methods of being able to measure Fe valence with very high spatial resolution across mineral grains and grain boundaries. We have modified an EELS method for point analyses of iron valence ratios (Fe 3+/ΣFe) making it possible to generate line scans and maps of Fe valence. We demonstrate this method with measurements at an interface between iron-bearing oxides in a finely intergrown sample of magnetite and ilmenite. The STEM/EELS method is based on a calibrated relationship between Fe 3+/ΣFe and the relative intensities of the Fe L 3 and L 2 white lines in core energy-loss spectra for oxide and silicate minerals. Our method overcomes problems of energy drift in spectrum images by aligning energy-loss edges at a fixed energy position prior to background removal. An automated routine for batch processing of core loss spectra, including additional background removal and calculation of Fe L 3/L 2 intensity ratios, allows for rapid Fe 3+/ΣFe determinations of multiple point analyses or spectrum images and the preparation of Fe valence maps, with an analytical error of ±0.05 to ±0.09 in the Fe 3+/ΣFe measurements.

Real-Time Measurements of Actin Filament Polymerization by Total Internal Reflection Fluorescence Microscopy

Understanding the mechanism of actin polymerization and its regulation by associated proteins requires an assay to monitor polymerization dynamics and filament topology simultaneously. The only assay meeting these criteria is total internal reflection fluorescence microscopy (Amann and Pollard, 2001; Fujiwara et al., 2002). The fluorescence signal is fourfold stronger with actin labeled on Cys-374 with Oregon green rather than rhodamine. To distinguish growth at barbed and pointed ends we used image drift correction and maximum intensity projections to reveal points where single N-ethylmaleimide inactivated myosins attach filaments to the glass coverslip. We estimated association rates at high actin concentrations and dissociation rates near and below the critical actin concentration. At the barbed end, the association rate constant for Mg-ATP-actin is 7.4μM−1s−1 and the dissociation rate constant is 0.89s−1. At the pointed end the association and dissociation rate constants are 0.56μM−1s−1 and 0.19s−1. When vitamin D binding protein sequesters all free monomers, ADP-actin dissociates from barbed ends at 1.4s−1 and from pointed ends at 0.16s−1 regardless of buffer nucleotide.

Spatially resolved tunneling spectroscopy on TTF-TCNQ

Local tunneling spectroscopy has been measured with low temperature UHV-STM on in-situ cleaved ab surface of organic TTF-TCNQ crystal. Due to ultra low image drift and clear molecular resolution, the spectroscopy is performed at specific molecular site either on TCNQ or TTF chains. In normal state (T= 63 K), a large pseudo-gap exists both in TTF and TCNQ chains. Above pseudo-gap local density of states differs for TTF and TCNQ chains that is in good agreement with double band model. By the signature of an anomalous in local spectroscopy measurement, a single impurity has been detected on a TTF chain. Charge density wave fluctuation is pinned by impurity above critical temperature (T=54K). Results obtained show that, Scanning Tunneling Spectroscopy can provide spatially resolved spectroscopic information at nanometer scale.

Segregation of object and background motion in the retina.

An important task in vision is to detect objects moving within a stationary scene. During normal viewing this is complicated by the presence of eye movements that continually scan the image across the retina, even during fixation. To detect moving objects, the brain must distinguish local motion within the scene from the global retinal image drift due to fixational eye movements. We have found that this process begins in the retina: a subset of retinal ganglion cells responds to motion in the receptive field centre, but only if the wider surround moves with a different trajectory. This selectivity for differential motion is independent of direction, and can be explained by a model of retinal circuitry that invokes pooling over nonlinear interneurons. The suppression by global image motion is probably mediated by polyaxonal, wide-field amacrine cells with transient responses. We show how a population of ganglion cells selective for differential motion can rapidly flag moving objects, and even segregate multiple moving objects.

Microtexture Measurement of Copper Damascene Line with EBSD

Microtexture of 0.18μm, 0.25μm, 0.70μm, and 2μm widths Cu damascene line is measured by EBSD technique. The image drift could be reduced by the shortening of measurement time, and could be completely removed by selected area mapping technique. Using carbon and gold dual layer coating method, image drift and pattern indexing fraction is improved but the EBSD pattern quality is decreased. By increasing the accelerating voltage from 15kV to 20kV, pattern quality loss could be compensated without resolution loss. Strong {111} texture is obtained in 0.18 and 0.25μm line, and weak {111} texture is observed in 2μm line. And every line was observed to have more than 60% CSL boundaries.

Medical treatment of nystagmus and its visual consequences

For us to see clearly the details in our visual world, images must be held quite still upon the retina, especially the central part (the fovea). For reading, which concerns detection of high spatial frequencies, image motion must be less than about 5° / second1. If image drift substantially exceeds this limit, visual acuity will decline and we may experience the illusion that the world is moving (oscillopsia). In health, three main mechanisms hold the line of sight steady so that our view of the world is clear and stable2. The first is ‘fixation’, which has two distinct components—the visual system's ability to detect retinal image drift and programme corrective eye movements, and the ability to suppress unwanted eye movements that would take the eye away from the target. The second mechanism is the vestibulo-ocular reflex, by which the motion detectors of the inner ear promptly initiate eye movements to compensate for head perturbations, such as occur during locomotion. The third mechanism is the gaze-holding system, which makes it possible to hold the eyes at an eccentric position (e.g. in lateral gaze). If any of the three mechanisms that normally act to hold gaze steady malfunctions, the eyes may start to drift away from the object of regard, and corrective rapid eye movements may be made. Thus, nystagmus may be defined as repetitive to-and-fro involuntary eye movements that are initiated by slow drifts of the eye. It is important to realize that some forms of nystagmus are normal. Thus, nystagmus that occurs during rotation of the body in space acts to preserve clear vision. In pathological nystagmus, however, drifts of the eyes away from the target degrade vision. In one form, pendular nystagmus, the drifts consist of a to-and-fro sinusoidal oscillation. More commonly, nystagmus consists of alternation of unidirectional drifts away from the target and corrective fast movements (saccades) which momentarily bring the visual target back to the fovea; this is jerk nystagmus. Nystagmus should be distinguished from inappropriate saccades that disrupt steady fixation. Saccades produce high-speed movement of images upon the retina—too high for clear vision—and several physiological mechanisms exist to prevent perception of the smeared retinal signal due to the saccade. However, patients in whom inappropriate saccades repeatedly misdirect the fovea often complain of difficulty with reading. Box 1 Medical strategies for treating nystagmus and its visual consequences Methods that place the eye in a position in which nystagmus is minimized Optical and electronic methods for negating the visual consequences of the nystagmus Procedures for weakening the extraocular muscles Application of somatosensory or auditory stimuli to suppress nystagmus Drugs that suppress some forms of nystagmus. Five main approaches to treating pathological nystagmus and its visual consequences are summarized in Box 1. For a fuller discussion of the clinical features, pathogenesis and treatment of nystagmus, the reader is referred to a recent textbook on eye movements2.

Cross-correlation image tracking for drift correction and adsorbate analysis

A digital image tracking algorithm based on Fourier-transform cross-correlation has been developed to correct for instrumental drift in scanning tunneling microscope images. A technique was developed to eliminate cumulative tracking errors associated with fractional pixel drift. This tracking algorithm was used to monitor conductance changes associated with different conformations in conjugated molecular switch molecules and to trace the diffusion of individual benzene molecules on Ag{110}. Molecular motions have been tracked for up to 25 h (400 images) of acquisition time.

Evaluation of image drift correction by three-dimensional Fourier analysis

Evaluation of image drift correction by three-dimensional Fourier analysis

Analyzing atomic force microscopy images using spectral methods

Various statistical quantities (such as average, peak-to-valley, and root-mean-square roughness) have been applied to characterize surface topography. However, they provide only vertical information. Because spectral analysis provides both lateral and longitudinal information, it is a more informative measurement than all these commonly used statistical quantities. Unfortunately, a standard method to calculate power spectral density (PSD) is not available. For example, the dimensions of PSD are often denoted as either (length)3 or (length)4. This may lead to confusion when utilizing spectral analysis to study surface morphology. In this paper, we will first compare the definitions of PSD commonly used by various authors. Using silicon surface roughness measurements as examples, we will demonstrate the advantages of spectral methods on atomic force microscopic (AFM) image analysis. In this context, we study the effects of typical AFM imaging distortions such as image bow, drift, tip-shape effects, and acoustic noise. As a result, we will provide a procedure to obtain accurate and reproducible AFM measurements.

The phase spectrum-based measurement of the TEM parameters

The phase spectrum-based method proposed by Koster et al. (Ultramicroscopy 27 (1989) 251) has experimentally been demonstrated by a computerized 200 kV transmission electron microscope with a slow-scan CCD camera system, which has theoretical advantages compared to other methods utilizing diffractograms. Crucial for the practical implementation of the method has been the addition of a linear phase term in the mathematical model made of the phase contrast transfer function to represent image drift. Moreover, to improve the accuracy of the method for measuring the TEM parameters (defocus, astigmatism and beam tilt misalignment), the model for least squares fitting was used in its full mathematical form without approximation by the DSB imaging model, neglecting the SSB imaging as was done in the original proposal. Experimental results of the TEM parameter measurements, defocus, astigmatism and beam tilt misalignment, by the phase spectrum-based method are demonstrated.

Simulation of Interstitial Cluster Mobility and Cluster Mediated Surface Topologies

ABSTRACTMolecular statics and molecular dynamics (MD) simulations based on the embedded atom method (EAM) are used to model the energetics and mobility of tightly bound clusters of selfinterstitial atoms (SIA) in bcc iron. Single and clusters of SIA are directly produced in displacement cascades generated in neutron and high energy charged particle beam irradiations. The clusters are composed of <111> split dumbbells and crowdions with binding energies in excess of 1 eV. Clusters containing specified ‘magic’ numbers of SIA can be described as perfect prismatic dislocation loops with Burgers vector b=a/2<111>; however, the core region is extended compared to an isolated edge dislocation and the loops are intrinsically kinked. As the loops grow, SIA occupy successive edge rows, with minimum energy cusps found at the magic numbers corresponding to filled hexagonal shells. The SIA clusters are highly mobile, undergoing rapid one-dimensional diffusion on their glide prism. The activation energy for glide diffusion is less than 0.3 eV and the corresponding mechanism is related to easy motion of the intrinsic kinks. The kinks, which are preferentially observed on the hexagonal corners, propagate around the loop periphery, resulting in stochastic increments of glide. Image drift forces bias cluster motion near free surfaces and the consequential annihilation of clusters at the surface produces islands bounded by hexagonal ledges. The potential effect of islands modifying surface topology is also discussed. While these simulations are specific to iron, similar behavior is expected for other cubic alloys.